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Molecular Modeling Database at NCBI

Tutorial and training materials by OpenHelix

Learn to use Molecular Modeling Database, or MMDB , which is Entrez's structural database brought to you by the National Institutes of Health and the National Center for Biotechnology Information. It contains an extensive collection of three-dimensional structures with detailed annotation that can be used to learn about the structure and function of many proteins. MMDB's structures were originally obtained from PBD and they contain descriptions, references and extensive multi-directional links both inside and outside of the NCBI network. There are pre-computed structural homologs, i.e. related structures or neighbors, that you can access, and extensive visualization and comparative analysis tools that you can use to examine individual structures, or multiple structures aligned.

You'll learn:

  • to search MMDB using both basic and advanced query techniques
  • how to understand the detailed results you obtain
  • methods to visualize and manipulate structures using NCBIs Cn3D structural viewer
  • to locate and view structurally aligned homologs


View additional tutorials for resources in

  • Proteins
  • NCBI : This category includes all resources maintained at the National Center for Biotechnology Information (NCBI)

Recent BioMed Central research articles citing this resource

Muñoz-Clares A Rosario et al., Exploring the evolutionary route of the acquisition of betaine aldehyde dehydrogenase activity by plant ALDH10 enzymes: implications for the synthesis of the osmoprotectant glycine betaine Genomics and evolution. BMC Plant Biology (2014) doi:10.1186/1471-2229-14-149

Wong Lok Kam et al., Bioactive proteins and peptides isolated from Chinese medicines with pharmaceutical potential. Chinese Medicine (2014) doi:10.1186/1749-8546-9-19

Newmaster G Steven et al., DNA barcoding detects contamination and substitution in North American herbal products. BMC Medicine (2013) doi:10.1186/1741-7015-11-222

Nagpure Sahebrao Naresh et al., FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent Comparative and evolutionary genomics. BMC Genomics (2013) doi:10.1186/1471-2164-14-630

Kim Sunghwan et al., PubChem3D: conformer ensemble accuracy. Journal of Cheminformatics (2013) doi:10.1186/1758-2946-5-1

More about the resource:

MMDB contains about 40,000 structures with detailed annotation for each. The database can be queried using basic and advanced searching techniques. Each structure has a structure summary page which presents references, ligands present, identifiers, structural homologs and graphical displays. There are many links both within and outside of NCBI's Entrez network of databases on these pages which allow you to find relevant information regarding domains, ligands, homologs, taxonomy and both protein and nucleotide sequences. You can download NCBIs structural viewer, Cn3D, for visualization and manipulation of the structures and you can also access the database of pre-computed structural homologs to align with your structures.

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The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.

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